Serial dilution curve: a new method for analysis of reverse phase protein array data

Reverse phase protein arrays (RPPAs) are a powerful high-throughput tool for measuring protein concentrations in a large number of samples. In RPPA technology, the original samples are often diluted successively multiple times, forming dilution series to extend the dynamic range of the measurements and to increase confidence in quantitation. An RPPA experiment is equivalent to running multiple ELISA assays concurrently except that there is usually no known protein concentration from which one can construct a standard response curve. Here, we describe a new method called ‘serial dilution curve for RPPA data analysis’. Compared with the existing methods, the new method has the advantage of using fewer parameters and offering a simple way of visualizing the raw data. We showed how the method can be used to examine data quality and to obtain robust quantification of protein concentrations. Availability: A computer program in R for using serial dilution curve for RPPA data analysis is freely available at http://odin.mdacc.tmc.edu/~zhangli/RPPA. Contact: lzhangli@mdanderson.org